/Engine/Plugins/Runtime/GeometryProcessing/Source/DynamicMesh/Public/Operations/MeshRegionOperator.h
This is very hard to remove, but we can at least avoid creating non-manifold edges (which with the current DMesh3 will be prevented, hence leaving a hole) by splitting the internal edge in the submesh (which presumably we were remeshing anyway, so changes are ok).
void RepairPossibleNonManifoldEdges()